public abstract class BioPolymer extends java.lang.Object implements Structure
Modifier and Type | Field and Description |
---|---|
int |
bioPolymerIndexInModel |
(package private) BS |
bsSelectedMonomers |
protected javajs.util.P3[] |
controlPoints |
protected boolean |
hasStructure |
protected boolean |
hasWingPoints |
boolean |
haveParameters |
protected boolean |
invalidControl |
private boolean |
invalidLead |
protected int[] |
leadAtomIndices |
protected javajs.util.P3[] |
leadMidpoints |
protected javajs.util.P3[] |
leadPoints |
Model |
model |
int |
monomerCount |
Monomer[] |
monomers |
BS |
reversed |
private int |
selectedMonomerCount |
protected float |
sheetSmoothing |
boolean |
twistedSheets |
protected int |
type |
protected static int |
TYPE_AMINO |
protected static int |
TYPE_CARBOHYDRATE |
protected static int |
TYPE_NOBONDING |
protected static int |
TYPE_NUCLEIC |
private javajs.util.V3 |
unitVectorX |
protected javajs.util.V3[] |
wingVectors |
Modifier | Constructor and Description |
---|---|
protected |
BioPolymer() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
calcEtaThetaAngles() |
private void |
calcLeadMidpointsAndWingVectors() |
boolean |
calcParameters() |
protected boolean |
calcPhiPsiAngles() |
void |
calcRasmolHydrogenBonds(BioPolymer polymer,
BS bsA,
BS bsB,
javajs.util.Lst<Bond> vHBonds,
int nMaxPerResidue,
int[][][] min,
boolean checkDistances,
boolean dsspIgnoreHydrogens) |
void |
calcSelectedMonomersCount(BS bsSelected) |
protected float |
calculateRamachandranHelixAngle(int m,
char qtype) |
void |
clearStructures() |
void |
findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
short[] mads,
int myVisibilityFlag,
BS bsNot) |
protected javajs.util.P3 |
getControlPoint(int i,
javajs.util.V3 v) |
javajs.util.P3[] |
getControlPoints(boolean isTraceAlpha,
float sheetSmoothing,
boolean invalidate) |
private javajs.util.P3[] |
getControlPoints2(float sheetSmoothing) |
protected int |
getIndex(int chainID,
int seqcode,
int istart,
int iend) |
private javajs.util.P3 |
getInitiatorPoint() |
int[] |
getLeadAtomIndices() |
(package private) void |
getLeadMidPoint(int i,
javajs.util.P3 midPoint) |
javajs.util.P3[] |
getLeadMidpoints() |
(package private) javajs.util.P3 |
getLeadPoint(int monomerIndex) |
(package private) javajs.util.P3[] |
getLeadPoints() |
int |
getPolymerPointsAndVectors(int last,
BS bs,
javajs.util.Lst<javajs.util.P3[]> vList,
boolean isTraceAlpha,
float sheetSmoothing) |
void |
getPolymerSequenceAtoms(int group1,
int nGroups,
BS bsInclude,
BS bsResult) |
ProteinStructure |
getProteinStructure(int monomerIndex) |
void |
getRange(BS bs,
boolean isMutated) |
void |
getRangeGroups(int nResidues,
BS bsAtoms,
BS bsResult) |
(package private) int |
getSelectedMonomerCount() |
java.lang.String |
getSequence() |
private javajs.util.P3 |
getTerminatorPoint() |
int |
getType() |
(package private) javajs.util.P3 |
getWingPoint(int polymerIndex) |
javajs.util.V3[] |
getWingVectors() |
(package private) boolean |
isMonomerSelected(int i) |
boolean |
isNucleic() |
void |
recalculateLeadMidpointsAndWingVectors() |
protected void |
resetHydrogenPoints() |
protected void |
set(Monomer[] monomers) |
void |
setAtomBits(BS bs) |
void |
setAtomBitsAndClear(BS bs,
BS bsOut) |
void |
setConformation(BS bsSelected) |
public Model model
public Monomer[] monomers
protected boolean hasStructure
protected javajs.util.P3[] leadMidpoints
protected javajs.util.P3[] leadPoints
protected javajs.util.P3[] controlPoints
protected javajs.util.V3[] wingVectors
protected int[] leadAtomIndices
protected int type
public int bioPolymerIndexInModel
public int monomerCount
protected static final int TYPE_NOBONDING
protected static final int TYPE_AMINO
protected static final int TYPE_NUCLEIC
protected static final int TYPE_CARBOHYDRATE
private boolean invalidLead
protected boolean invalidControl
protected float sheetSmoothing
protected boolean hasWingPoints
public BS reversed
public boolean twistedSheets
private final javajs.util.V3 unitVectorX
private int selectedMonomerCount
BS bsSelectedMonomers
public boolean haveParameters
protected void set(Monomer[] monomers)
public void setAtomBits(BS bs)
setAtomBits
in interface Structure
public void setAtomBitsAndClear(BS bs, BS bsOut)
setAtomBitsAndClear
in interface Structure
public void getRange(BS bs, boolean isMutated)
public void clearStructures()
public int[] getLeadAtomIndices()
protected int getIndex(int chainID, int seqcode, int istart, int iend)
final javajs.util.P3 getLeadPoint(int monomerIndex)
private final javajs.util.P3 getInitiatorPoint()
private final javajs.util.P3 getTerminatorPoint()
void getLeadMidPoint(int i, javajs.util.P3 midPoint)
final javajs.util.P3 getWingPoint(int polymerIndex)
public void setConformation(BS bsSelected)
public void recalculateLeadMidpointsAndWingVectors()
protected void resetHydrogenPoints()
public javajs.util.P3[] getLeadMidpoints()
javajs.util.P3[] getLeadPoints()
public javajs.util.P3[] getControlPoints(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate)
private javajs.util.P3[] getControlPoints2(float sheetSmoothing)
protected javajs.util.P3 getControlPoint(int i, javajs.util.V3 v)
i
- v
- public final javajs.util.V3[] getWingVectors()
private final void calcLeadMidpointsAndWingVectors()
public void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag, BS bsNot)
int getSelectedMonomerCount()
public void calcSelectedMonomersCount(BS bsSelected)
boolean isMonomerSelected(int i)
public int getPolymerPointsAndVectors(int last, BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
public java.lang.String getSequence()
public void getPolymerSequenceAtoms(int group1, int nGroups, BS bsInclude, BS bsResult)
public ProteinStructure getProteinStructure(int monomerIndex)
monomerIndex
- public boolean calcParameters()
protected boolean calcEtaThetaAngles()
protected boolean calcPhiPsiAngles()
protected float calculateRamachandranHelixAngle(int m, char qtype)
m
- qtype
- public boolean isNucleic()
public void calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
polymer
- bsA
- bsB
- vHBonds
- nMaxPerResidue
- min
- checkDistances
- dsspIgnoreHydrogens
- public int getType()